Starting phenix.real_space_refine on Wed Mar 4 22:01:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6oes_20036/03_2026/6oes_20036.cif Found real_map, /net/cci-nas-00/data/ceres_data/6oes_20036/03_2026/6oes_20036.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6oes_20036/03_2026/6oes_20036.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6oes_20036/03_2026/6oes_20036.map" model { file = "/net/cci-nas-00/data/ceres_data/6oes_20036/03_2026/6oes_20036.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6oes_20036/03_2026/6oes_20036.cif" } resolution = 3.06 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Ca 2 9.91 5 Zn 2 6.06 5 P 126 5.49 5 S 103 5.16 5 C 10243 2.51 5 N 2954 2.21 5 O 3399 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16829 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 4411 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 548, 4405 Classifications: {'peptide': 548} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 522} Conformer: "B" Number of residues, atoms: 548, 4405 Classifications: {'peptide': 548} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 522} bond proxies already assigned to first conformer: 4495 Chain: "B" Number of atoms: 2708 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 344, 2679 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 19, 'TRANS': 324} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Conformer: "B" Number of residues, atoms: 344, 2679 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 19, 'TRANS': 324} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 bond proxies already assigned to first conformer: 2714 Chain: "C" Number of atoms: 4397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 547, 4397 Classifications: {'peptide': 547} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 521} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 2687 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 345, 2677 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 19, 'TRANS': 325} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Conformer: "B" Number of residues, atoms: 345, 2677 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 19, 'TRANS': 325} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 bond proxies already assigned to first conformer: 2733 Chain: "F" Number of atoms: 722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 722 Classifications: {'DNA': 35} Link IDs: {'rna3p': 34} Chain: "J" Number of atoms: 303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 303 Classifications: {'DNA': 15} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 14} Chain: "I" Number of atoms: 303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 303 Classifications: {'DNA': 15} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 14} Chain: "G" Number of atoms: 695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 695 Classifications: {'DNA': 34} Link IDs: {'rna3p': 33} Chain: "L" Number of atoms: 307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 307 Classifications: {'DNA': 15} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 14} Chain: "M" Number of atoms: 290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 290 Classifications: {'DNA': 14} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 13} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2074 SG CYS A 727 77.316 60.140 63.274 1.00 35.24 S ATOM 2095 SG CYS A 730 79.566 57.590 65.579 1.00 38.04 S ATOM 9193 SG CYS C 727 24.484 103.311 59.410 1.00 35.23 S ATOM 9214 SG CYS C 730 21.682 105.123 61.104 1.00 37.28 S Residues with excluded nonbonded symmetry interactions: 7 residue: pdb=" N ACYS A 907 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS A 907 " occ=0.50 residue: pdb=" N AHIS B 47 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS B 47 " occ=0.50 residue: pdb=" N AARG B 237 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG B 237 " occ=0.50 residue: pdb=" N AASN B 268 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN B 268 " occ=0.50 residue: pdb=" N AHIS D 47 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS D 47 " occ=0.50 residue: pdb=" P DT J 15 " occ=0.85 ... (18 atoms not shown) pdb=" C6 DT J 15 " occ=0.85 residue: pdb=" P DT I 15 " occ=0.85 ... (18 atoms not shown) pdb=" C6 DT I 15 " occ=0.85 Time building chain proxies: 5.15, per 1000 atoms: 0.31 Number of scatterers: 16829 At special positions: 0 Unit cell: (105.93, 159.43, 119.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 Ca 2 19.99 S 103 16.00 P 126 15.00 O 3399 8.00 N 2954 7.00 C 10243 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.92 Conformation dependent library (CDL) restraints added in 847.9 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1102 " pdb="ZN ZN A1102 " - pdb=" NE2 HIS A 937 " pdb="ZN ZN A1102 " - pdb=" NE2 HIS A 942 " pdb="ZN ZN A1102 " - pdb=" SG CYS A 727 " pdb="ZN ZN A1102 " - pdb=" SG CYS A 730 " pdb=" ZN C1102 " pdb="ZN ZN C1102 " - pdb=" NE2 HIS C 942 " pdb="ZN ZN C1102 " - pdb=" NE2 HIS C 937 " pdb="ZN ZN C1102 " - pdb=" SG CYS C 727 " pdb="ZN ZN C1102 " - pdb=" SG CYS C 730 " Number of angles added : 4 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3350 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 17 sheets defined 34.2% alpha, 24.3% beta 61 base pairs and 103 stacking pairs defined. Time for finding SS restraints: 2.31 Creating SS restraints... Processing helix chain 'A' and resid 463 through 474 Processing helix chain 'A' and resid 477 through 493 removed outlier: 3.787A pdb=" N LYS A 483 " --> pdb=" O SER A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 507 Processing helix chain 'A' and resid 558 through 581 removed outlier: 5.440A pdb=" N GLU A 572 " --> pdb=" O MET A 568 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N ASP A 573 " --> pdb=" O ASP A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 682 Proline residue: A 674 - end of helix Processing helix chain 'A' and resid 683 through 685 No H-bonds generated for 'chain 'A' and resid 683 through 685' Processing helix chain 'A' and resid 708 through 716 Processing helix chain 'A' and resid 733 through 741 removed outlier: 3.648A pdb=" N GLN A 739 " --> pdb=" O LEU A 735 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 763 Processing helix chain 'A' and resid 768 through 777 Processing helix chain 'A' and resid 792 through 812 Processing helix chain 'A' and resid 822 through 841 removed outlier: 3.658A pdb=" N ARG A 826 " --> pdb=" O SER A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 858 Processing helix chain 'A' and resid 859 through 868 Processing helix chain 'A' and resid 873 through 890 Processing helix chain 'A' and resid 891 through 893 No H-bonds generated for 'chain 'A' and resid 891 through 893' Processing helix chain 'A' and resid 902 through 908 Processing helix chain 'A' and resid 908 through 923 Processing helix chain 'A' and resid 933 through 942 removed outlier: 3.614A pdb=" N HIS A 942 " --> pdb=" O LYS A 938 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 951 Processing helix chain 'A' and resid 958 through 975 removed outlier: 3.663A pdb=" N ARG A 969 " --> pdb=" O ASN A 965 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ARG A 970 " --> pdb=" O LYS A 966 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 995 removed outlier: 3.537A pdb=" N ASP A 986 " --> pdb=" O TYR A 982 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR A 995 " --> pdb=" O HIS A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 996 through 1001 removed outlier: 3.593A pdb=" N LYS A1001 " --> pdb=" O LYS A 997 " (cutoff:3.500A) Processing helix chain 'A' and resid 1002 through 1005 removed outlier: 3.621A pdb=" N ALA A1005 " --> pdb=" O PHE A1002 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1002 through 1005' Processing helix chain 'B' and resid 11 through 15 removed outlier: 3.661A pdb=" N LEU B 14 " --> pdb=" O ASN B 11 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE B 15 " --> pdb=" O ILE B 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 11 through 15' Processing helix chain 'B' and resid 168 through 172 removed outlier: 3.838A pdb=" N TRP B 172 " --> pdb=" O THR B 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 463 through 474 Processing helix chain 'C' and resid 477 through 493 Processing helix chain 'C' and resid 499 through 508 removed outlier: 3.531A pdb=" N LYS C 508 " --> pdb=" O ARG C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 558 through 569 Processing helix chain 'C' and resid 570 through 581 removed outlier: 3.503A pdb=" N GLN C 581 " --> pdb=" O GLY C 577 " (cutoff:3.500A) Processing helix chain 'C' and resid 664 through 683 Proline residue: C 674 - end of helix Processing helix chain 'C' and resid 708 through 716 Processing helix chain 'C' and resid 733 through 740 Processing helix chain 'C' and resid 749 through 763 Processing helix chain 'C' and resid 768 through 777 Processing helix chain 'C' and resid 792 through 813 removed outlier: 3.658A pdb=" N GLY C 813 " --> pdb=" O GLN C 809 " (cutoff:3.500A) Processing helix chain 'C' and resid 822 through 840 Processing helix chain 'C' and resid 850 through 858 Processing helix chain 'C' and resid 859 through 867 removed outlier: 3.568A pdb=" N VAL C 863 " --> pdb=" O THR C 859 " (cutoff:3.500A) Processing helix chain 'C' and resid 872 through 895 removed outlier: 3.630A pdb=" N HIS C 876 " --> pdb=" O SER C 872 " (cutoff:3.500A) Proline residue: C 891 - end of helix Processing helix chain 'C' and resid 897 through 902 removed outlier: 3.518A pdb=" N CYS C 902 " --> pdb=" O PRO C 898 " (cutoff:3.500A) Processing helix chain 'C' and resid 902 through 908 removed outlier: 3.726A pdb=" N GLN C 908 " --> pdb=" O GLU C 904 " (cutoff:3.500A) Processing helix chain 'C' and resid 908 through 923 Processing helix chain 'C' and resid 933 through 942 removed outlier: 3.540A pdb=" N HIS C 942 " --> pdb=" O LYS C 938 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 950 Processing helix chain 'C' and resid 958 through 975 removed outlier: 4.050A pdb=" N LYS C 973 " --> pdb=" O ARG C 969 " (cutoff:3.500A) Processing helix chain 'C' and resid 982 through 995 removed outlier: 3.546A pdb=" N ASP C 986 " --> pdb=" O TYR C 982 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR C 995 " --> pdb=" O HIS C 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 996 through 1001 Processing helix chain 'C' and resid 1002 through 1005 removed outlier: 3.688A pdb=" N ALA C1005 " --> pdb=" O PHE C1002 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1002 through 1005' Processing helix chain 'D' and resid 11 through 15 removed outlier: 3.662A pdb=" N LEU D 14 " --> pdb=" O ASN D 11 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 172 removed outlier: 3.838A pdb=" N TRP D 172 " --> pdb=" O THR D 169 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 517 through 520 removed outlier: 3.702A pdb=" N ILE A 694 " --> pdb=" O MET A 691 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N PHE A 591 " --> pdb=" O LYS A 699 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N ILE A 701 " --> pdb=" O PHE A 591 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N VAL A 593 " --> pdb=" O ILE A 701 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N ARG A 703 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N VAL A 595 " --> pdb=" O ARG A 703 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N THR A 705 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N GLU A 597 " --> pdb=" O THR A 705 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N ILE A 631 " --> pdb=" O PRO A 590 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N THR A 592 " --> pdb=" O ILE A 629 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ILE A 629 " --> pdb=" O THR A 592 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N VAL A 594 " --> pdb=" O MET A 627 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N PHE A 624 " --> pdb=" O PRO A 654 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 517 through 520 removed outlier: 3.702A pdb=" N ILE A 694 " --> pdb=" O MET A 691 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N PHE A 591 " --> pdb=" O LYS A 699 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N ILE A 701 " --> pdb=" O PHE A 591 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N VAL A 593 " --> pdb=" O ILE A 701 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N ARG A 703 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N VAL A 595 " --> pdb=" O ARG A 703 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N THR A 705 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N GLU A 597 " --> pdb=" O THR A 705 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N ILE A 631 " --> pdb=" O PRO A 590 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N THR A 592 " --> pdb=" O ILE A 629 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ILE A 629 " --> pdb=" O THR A 592 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N VAL A 594 " --> pdb=" O MET A 627 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N MET A 627 " --> pdb=" O GLU A 642 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N GLU A 642 " --> pdb=" O MET A 627 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ILE A 629 " --> pdb=" O VAL A 640 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 2 through 5 removed outlier: 3.564A pdb=" N SER B 2 " --> pdb=" O ARG B 349 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE B 318 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 7 through 8 removed outlier: 6.783A pdb=" N THR B 7 " --> pdb=" O LEU B 55 " (cutoff:3.500A) removed outlier: 8.256A pdb=" N LEU B 57 " --> pdb=" O THR B 7 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASP B 49 " --> pdb=" O LYS B 56 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS B 58 " --> pdb=" O AHIS B 47 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N VAL B 28 " --> pdb=" O PHE B 48 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 76 through 80 removed outlier: 4.268A pdb=" N ILE B 107 " --> pdb=" O LYS B 127 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N THR B 121 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N LYS B 115 " --> pdb=" O LYS B 119 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N LYS B 119 " --> pdb=" O LYS B 115 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 130 through 131 removed outlier: 6.719A pdb=" N VAL B 130 " --> pdb=" O ALA B 192 " (cutoff:3.500A) removed outlier: 8.676A pdb=" N SER B 194 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N CYS B 191 " --> pdb=" O ASP B 186 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N SER B 141 " --> pdb=" O PHE B 156 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 159 through 161 Processing sheet with id=AA8, first strand: chain 'B' and resid 208 through 211 removed outlier: 4.010A pdb=" N LEU B 233 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 262 through 267 removed outlier: 3.511A pdb=" N THR B 266 " --> pdb=" O GLU B 270 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N GLU B 270 " --> pdb=" O THR B 266 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU B 298 " --> pdb=" O SER B 291 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 518 through 519 removed outlier: 3.544A pdb=" N ILE C 694 " --> pdb=" O MET C 691 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR C 705 " --> pdb=" O GLU C 597 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N CYS C 599 " --> pdb=" O THR C 705 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N VAL C 620 " --> pdb=" O LEU C 657 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N LEU C 657 " --> pdb=" O VAL C 620 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N PHE C 622 " --> pdb=" O LEU C 655 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 518 through 519 removed outlier: 3.544A pdb=" N ILE C 694 " --> pdb=" O MET C 691 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR C 705 " --> pdb=" O GLU C 597 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N CYS C 599 " --> pdb=" O THR C 705 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLU C 632 " --> pdb=" O PRO C 590 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG C 628 " --> pdb=" O VAL C 594 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LYS C 596 " --> pdb=" O VAL C 626 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N VAL C 626 " --> pdb=" O LYS C 596 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N MET C 627 " --> pdb=" O GLU C 642 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N GLU C 642 " --> pdb=" O MET C 627 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ILE C 629 " --> pdb=" O VAL C 640 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN C 636 " --> pdb=" O HIS C 633 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 20 through 24 removed outlier: 4.189A pdb=" N VAL D 28 " --> pdb=" O PHE D 48 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS D 58 " --> pdb=" O AHIS D 47 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASP D 49 " --> pdb=" O LYS D 56 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N LEU D 55 " --> pdb=" O MET D 5 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N THR D 7 " --> pdb=" O LEU D 55 " (cutoff:3.500A) removed outlier: 8.256A pdb=" N LEU D 57 " --> pdb=" O THR D 7 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER D 2 " --> pdb=" O ARG D 349 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N PHE D 345 " --> pdb=" O VAL D 6 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N VAL D 8 " --> pdb=" O PHE D 343 " (cutoff:3.500A) removed outlier: 10.111A pdb=" N PHE D 343 " --> pdb=" O VAL D 8 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE D 318 " --> pdb=" O GLY D 330 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 76 through 80 removed outlier: 4.268A pdb=" N ILE D 107 " --> pdb=" O LYS D 127 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N THR D 121 " --> pdb=" O ALA D 113 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N LYS D 115 " --> pdb=" O LYS D 119 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N LYS D 119 " --> pdb=" O LYS D 115 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 130 through 131 removed outlier: 6.718A pdb=" N VAL D 130 " --> pdb=" O ALA D 192 " (cutoff:3.500A) removed outlier: 8.677A pdb=" N SER D 194 " --> pdb=" O VAL D 130 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N CYS D 191 " --> pdb=" O ASP D 186 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N SER D 141 " --> pdb=" O PHE D 156 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 159 through 161 Processing sheet with id=AB7, first strand: chain 'D' and resid 208 through 211 removed outlier: 4.011A pdb=" N LEU D 233 " --> pdb=" O LEU D 252 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 262 through 267 removed outlier: 3.510A pdb=" N THR D 266 " --> pdb=" O GLU D 270 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N GLU D 270 " --> pdb=" O THR D 266 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU D 298 " --> pdb=" O SER D 291 " (cutoff:3.500A) 643 hydrogen bonds defined for protein. 1815 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 157 hydrogen bonds 314 hydrogen bond angles 0 basepair planarities 61 basepair parallelities 103 stacking parallelities Total time for adding SS restraints: 3.62 Time building geometry restraints manager: 1.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3963 1.33 - 1.45: 4431 1.45 - 1.58: 8674 1.58 - 1.70: 249 1.70 - 1.82: 157 Bond restraints: 17474 Sorted by residual: bond pdb=" N GLU B 341 " pdb=" CA GLU B 341 " ideal model delta sigma weight residual 1.457 1.498 -0.041 1.29e-02 6.01e+03 1.00e+01 bond pdb=" N GLU D 341 " pdb=" CA GLU D 341 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.29e-02 6.01e+03 9.16e+00 bond pdb=" N ASN D 335 " pdb=" CA ASN D 335 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.29e-02 6.01e+03 9.05e+00 bond pdb=" N LYS B 336 " pdb=" CA LYS B 336 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.29e-02 6.01e+03 8.68e+00 bond pdb=" O3' DC L 17 " pdb=" P DA L 18 " ideal model delta sigma weight residual 1.607 1.565 0.042 1.50e-02 4.44e+03 7.87e+00 ... (remaining 17469 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 23417 1.94 - 3.88: 666 3.88 - 5.82: 65 5.82 - 7.76: 19 7.76 - 9.70: 11 Bond angle restraints: 24178 Sorted by residual: angle pdb=" CB GLN D 201 " pdb=" CG GLN D 201 " pdb=" CD GLN D 201 " ideal model delta sigma weight residual 112.60 122.00 -9.40 1.70e+00 3.46e-01 3.06e+01 angle pdb=" CB GLN B 201 " pdb=" CG GLN B 201 " pdb=" CD GLN B 201 " ideal model delta sigma weight residual 112.60 121.99 -9.39 1.70e+00 3.46e-01 3.05e+01 angle pdb=" C ASP C 569 " pdb=" CA ASP C 569 " pdb=" CB ASP C 569 " ideal model delta sigma weight residual 110.01 119.06 -9.05 1.80e+00 3.09e-01 2.53e+01 angle pdb=" CA GLU D 301 " pdb=" CB GLU D 301 " pdb=" CG GLU D 301 " ideal model delta sigma weight residual 114.10 123.66 -9.56 2.00e+00 2.50e-01 2.28e+01 angle pdb=" CA GLU B 301 " pdb=" CB GLU B 301 " pdb=" CG GLU B 301 " ideal model delta sigma weight residual 114.10 123.64 -9.54 2.00e+00 2.50e-01 2.28e+01 ... (remaining 24173 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 8407 17.90 - 35.79: 1039 35.79 - 53.69: 571 53.69 - 71.58: 110 71.58 - 89.48: 15 Dihedral angle restraints: 10142 sinusoidal: 4936 harmonic: 5206 Sorted by residual: dihedral pdb=" C ASP C 569 " pdb=" N ASP C 569 " pdb=" CA ASP C 569 " pdb=" CB ASP C 569 " ideal model delta harmonic sigma weight residual -122.60 -136.16 13.56 0 2.50e+00 1.60e-01 2.94e+01 dihedral pdb=" C ASN D 335 " pdb=" N ASN D 335 " pdb=" CA ASN D 335 " pdb=" CB ASN D 335 " ideal model delta harmonic sigma weight residual -122.60 -133.49 10.89 0 2.50e+00 1.60e-01 1.90e+01 dihedral pdb=" N ASN D 335 " pdb=" C ASN D 335 " pdb=" CA ASN D 335 " pdb=" CB ASN D 335 " ideal model delta harmonic sigma weight residual 122.80 133.37 -10.57 0 2.50e+00 1.60e-01 1.79e+01 ... (remaining 10139 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 2375 0.083 - 0.165: 251 0.165 - 0.248: 13 0.248 - 0.330: 0 0.330 - 0.413: 2 Chirality restraints: 2641 Sorted by residual: chirality pdb=" CA ASP C 569 " pdb=" N ASP C 569 " pdb=" C ASP C 569 " pdb=" CB ASP C 569 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.26e+00 chirality pdb=" CA ASN D 335 " pdb=" N ASN D 335 " pdb=" C ASN D 335 " pdb=" CB ASN D 335 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.39e+00 chirality pdb=" CA LYS D 336 " pdb=" N LYS D 336 " pdb=" C LYS D 336 " pdb=" CB LYS D 336 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.29e+00 ... (remaining 2638 not shown) Planarity restraints: 2672 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 317 " 0.018 2.00e-02 2.50e+03 1.68e-02 7.08e+00 pdb=" CG TRP D 317 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 TRP D 317 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP D 317 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP D 317 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D 317 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 317 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 317 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 317 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP D 317 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 317 " 0.018 2.00e-02 2.50e+03 1.67e-02 6.97e+00 pdb=" CG TRP B 317 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 TRP B 317 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP B 317 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 317 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP B 317 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 317 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 317 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 317 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP B 317 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE D 331 " 0.011 2.00e-02 2.50e+03 2.25e-02 5.06e+00 pdb=" C ILE D 331 " -0.039 2.00e-02 2.50e+03 pdb=" O ILE D 331 " 0.014 2.00e-02 2.50e+03 pdb=" N PRO D 332 " 0.013 2.00e-02 2.50e+03 ... (remaining 2669 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2485 2.76 - 3.30: 13805 3.30 - 3.83: 29361 3.83 - 4.37: 35133 4.37 - 4.90: 58523 Nonbonded interactions: 139307 Sorted by model distance: nonbonded pdb=" O SER B 340 " pdb=" OG SER B 340 " model vdw 2.226 3.040 nonbonded pdb=" N GLY B 333 " pdb=" O ALA B 342 " model vdw 2.263 3.120 nonbonded pdb=" OD1 ASP B 143 " pdb=" OG SER B 209 " model vdw 2.275 3.040 nonbonded pdb=" OD1 ASP D 143 " pdb=" OG SER D 209 " model vdw 2.275 3.040 nonbonded pdb=" OH TYR C 805 " pdb=" OD1 ASP C 834 " model vdw 2.314 3.040 ... (remaining 139302 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 461 through 906 or resid 908 through 1006 or (resid 1007 a \ nd (name N or name CA or name C or name O or name CB )) or resid 1101 through 11 \ 02)) selection = (chain 'C' and (resid 461 through 906 or resid 908 through 1102)) } ncs_group { reference = (chain 'B' and (resid 1 through 46 or resid 48 through 117 or (resid 118 and (na \ me N or name CA or name C or name O or name CB )) or resid 119 through 236 or re \ sid 238 through 267 or resid 269 through 333 or (resid 334 and (name N or name C \ A or name C or name O or name CB )) or resid 335 through 350)) selection = (chain 'D' and (resid 1 through 46 or resid 48 through 236 or resid 238 through \ 267 or resid 269 through 350)) } ncs_group { reference = (chain 'F' and (resid 19 through 20 or resid 22 through 32 or resid 34 through 5 \ 0)) selection = (chain 'G' and (resid 30 through 31 or resid 33 through 43 or resid 45 through 6 \ 1)) } ncs_group { reference = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 20.600 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.167 17482 Z= 0.264 Angle : 0.790 17.581 24182 Z= 0.448 Chirality : 0.050 0.413 2641 Planarity : 0.006 0.055 2672 Dihedral : 19.675 89.477 6792 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.39 % Favored : 96.44 % Rotamer: Outliers : 2.87 % Allowed : 4.47 % Favored : 92.66 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.12 (0.16), residues: 1787 helix: -2.15 (0.15), residues: 558 sheet: -1.02 (0.26), residues: 349 loop : -2.43 (0.17), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 734 TYR 0.019 0.002 TYR A 757 PHE 0.016 0.002 PHE A 916 TRP 0.045 0.003 TRP D 317 HIS 0.005 0.001 HIS A 836 Details of bonding type rmsd covalent geometry : bond 0.00527 (17474) covalent geometry : angle 0.76806 (24178) hydrogen bonds : bond 0.17389 ( 768) hydrogen bonds : angle 6.98746 ( 2129) metal coordination : bond 0.14798 ( 8) metal coordination : angle 14.28898 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 253 time to evaluate : 0.373 Fit side-chains REVERT: A 602 MET cc_start: 0.8385 (mtp) cc_final: 0.8082 (mtp) REVERT: A 970 ARG cc_start: 0.8261 (ttt180) cc_final: 0.8056 (ttt180) REVERT: B 22 MET cc_start: 0.8383 (ptp) cc_final: 0.8134 (ptp) REVERT: B 223 SER cc_start: 0.8891 (OUTLIER) cc_final: 0.8529 (m) REVERT: B 347 THR cc_start: 0.8445 (OUTLIER) cc_final: 0.8177 (m) REVERT: C 568 MET cc_start: 0.8204 (mmm) cc_final: 0.7989 (tpt) REVERT: C 617 GLU cc_start: 0.7745 (mt-10) cc_final: 0.7490 (mt-10) REVERT: C 649 GLU cc_start: 0.7847 (pm20) cc_final: 0.7613 (pm20) REVERT: C 889 MET cc_start: 0.8490 (mtp) cc_final: 0.8137 (mtp) REVERT: D 22 MET cc_start: 0.8876 (ptp) cc_final: 0.8649 (ptp) REVERT: D 114 CYS cc_start: 0.7703 (p) cc_final: 0.7457 (p) REVERT: D 300 SER cc_start: 0.8117 (OUTLIER) cc_final: 0.7837 (m) outliers start: 43 outliers final: 11 residues processed: 282 average time/residue: 0.1467 time to fit residues: 60.1444 Evaluate side-chains 176 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 162 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 309 SER Chi-restraints excluded: chain B residue 339 MET Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain C residue 569 ASP Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 300 SER Chi-restraints excluded: chain D residue 335 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.0370 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 0.5980 chunk 149 optimal weight: 0.5980 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 750 HIS A 753 ASN A 961 ASN ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 54 HIS B 101 ASN B 181 HIS ** C 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 750 HIS C 820 ASN C 961 ASN C 965 ASN C1004 ASN D 54 HIS D 181 HIS D 268 ASN D 321 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.134709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.107812 restraints weight = 62600.883| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 2.72 r_work: 0.3087 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3086 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3086 r_free = 0.3086 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3084 r_free = 0.3084 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3084 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17482 Z= 0.131 Angle : 0.550 7.261 24182 Z= 0.306 Chirality : 0.041 0.177 2641 Planarity : 0.005 0.053 2672 Dihedral : 20.976 66.074 3334 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.10 % Favored : 96.73 % Rotamer: Outliers : 1.02 % Allowed : 9.00 % Favored : 89.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.19), residues: 1787 helix: 0.13 (0.21), residues: 567 sheet: -0.16 (0.28), residues: 336 loop : -1.74 (0.19), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 494 TYR 0.015 0.001 TYR A 757 PHE 0.025 0.001 PHE A 911 TRP 0.030 0.002 TRP B 317 HIS 0.003 0.001 HIS C 990 Details of bonding type rmsd covalent geometry : bond 0.00286 (17474) covalent geometry : angle 0.54857 (24178) hydrogen bonds : bond 0.03955 ( 768) hydrogen bonds : angle 4.68499 ( 2129) metal coordination : bond 0.01218 ( 8) metal coordination : angle 3.54743 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 177 time to evaluate : 0.613 Fit side-chains REVERT: A 602 MET cc_start: 0.8734 (mtp) cc_final: 0.8464 (mtp) REVERT: A 939 THR cc_start: 0.8945 (m) cc_final: 0.8710 (p) REVERT: C 649 GLU cc_start: 0.8153 (pm20) cc_final: 0.7878 (pm20) REVERT: C 858 MET cc_start: 0.8751 (mmt) cc_final: 0.8459 (mmp) REVERT: C 889 MET cc_start: 0.8607 (mtp) cc_final: 0.8294 (mtp) REVERT: D 285 MET cc_start: 0.8486 (mmm) cc_final: 0.8273 (mmm) outliers start: 14 outliers final: 8 residues processed: 187 average time/residue: 0.1424 time to fit residues: 39.4302 Evaluate side-chains 159 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 151 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 309 SER Chi-restraints excluded: chain C residue 553 ILE Chi-restraints excluded: chain C residue 973 LYS Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 295 ASN Chi-restraints excluded: chain D residue 317 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 142 optimal weight: 3.9990 chunk 178 optimal weight: 3.9990 chunk 161 optimal weight: 5.9990 chunk 108 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 128 optimal weight: 0.6980 chunk 24 optimal weight: 0.4980 chunk 169 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 473 ASN ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 495 GLN C 498 GLN C 961 ASN D 52 GLN D 278 GLN D 282 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.130773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.103659 restraints weight = 64262.632| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 2.67 r_work: 0.3032 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3038 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3038 r_free = 0.3038 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3038 r_free = 0.3038 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3038 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 17482 Z= 0.190 Angle : 0.577 8.261 24182 Z= 0.315 Chirality : 0.043 0.175 2641 Planarity : 0.005 0.044 2672 Dihedral : 21.177 72.406 3320 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.72 % Favored : 96.22 % Rotamer: Outliers : 1.79 % Allowed : 11.43 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.19), residues: 1787 helix: 0.75 (0.22), residues: 575 sheet: 0.08 (0.28), residues: 326 loop : -1.51 (0.19), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 848 TYR 0.017 0.001 TYR A 805 PHE 0.026 0.002 PHE A 911 TRP 0.040 0.002 TRP B 317 HIS 0.006 0.001 HIS C 990 Details of bonding type rmsd covalent geometry : bond 0.00445 (17474) covalent geometry : angle 0.57349 (24178) hydrogen bonds : bond 0.04099 ( 768) hydrogen bonds : angle 4.42435 ( 2129) metal coordination : bond 0.01278 ( 8) metal coordination : angle 5.30931 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 156 time to evaluate : 0.508 Fit side-chains REVERT: A 602 MET cc_start: 0.8703 (mtp) cc_final: 0.8378 (mtp) REVERT: A 939 THR cc_start: 0.9059 (m) cc_final: 0.8757 (p) REVERT: B 5 MET cc_start: 0.8220 (ttp) cc_final: 0.8018 (ttt) REVERT: B 55 LEU cc_start: 0.9130 (tp) cc_final: 0.8914 (tp) REVERT: C 649 GLU cc_start: 0.8236 (pm20) cc_final: 0.8010 (pm20) REVERT: C 858 MET cc_start: 0.8821 (mmt) cc_final: 0.8474 (mmp) REVERT: C 889 MET cc_start: 0.8664 (mtp) cc_final: 0.8270 (mtt) outliers start: 26 outliers final: 18 residues processed: 178 average time/residue: 0.1337 time to fit residues: 35.8995 Evaluate side-chains 166 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 148 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 520 GLN Chi-restraints excluded: chain B residue 101 ASN Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 287 CYS Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain C residue 553 ILE Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 631 ILE Chi-restraints excluded: chain C residue 697 THR Chi-restraints excluded: chain C residue 961 ASN Chi-restraints excluded: chain C residue 973 LYS Chi-restraints excluded: chain C residue 995 THR Chi-restraints excluded: chain D residue 295 ASN Chi-restraints excluded: chain D residue 298 GLU Chi-restraints excluded: chain D residue 326 THR Chi-restraints excluded: chain D residue 329 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 137 optimal weight: 6.9990 chunk 143 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 79 optimal weight: 0.4980 chunk 61 optimal weight: 0.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 4 GLN ** C 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 961 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.131830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.104575 restraints weight = 60561.603| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 2.54 r_work: 0.3043 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3047 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3047 r_free = 0.3047 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3047 r_free = 0.3047 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3047 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 17482 Z= 0.157 Angle : 0.544 8.994 24182 Z= 0.298 Chirality : 0.041 0.169 2641 Planarity : 0.004 0.044 2672 Dihedral : 21.121 75.198 3316 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.56 % Favored : 96.39 % Rotamer: Outliers : 2.23 % Allowed : 11.62 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.20), residues: 1787 helix: 1.12 (0.22), residues: 568 sheet: 0.22 (0.28), residues: 337 loop : -1.32 (0.20), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 148 TYR 0.015 0.001 TYR A 757 PHE 0.028 0.001 PHE A 911 TRP 0.028 0.002 TRP B 317 HIS 0.004 0.001 HIS C 990 Details of bonding type rmsd covalent geometry : bond 0.00364 (17474) covalent geometry : angle 0.54091 (24178) hydrogen bonds : bond 0.03626 ( 768) hydrogen bonds : angle 4.26995 ( 2129) metal coordination : bond 0.01006 ( 8) metal coordination : angle 4.60270 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 157 time to evaluate : 0.594 Fit side-chains REVERT: A 602 MET cc_start: 0.8653 (mtp) cc_final: 0.8345 (mtp) REVERT: A 939 THR cc_start: 0.9101 (m) cc_final: 0.8814 (p) REVERT: B 55 LEU cc_start: 0.9127 (tp) cc_final: 0.8876 (tp) REVERT: C 649 GLU cc_start: 0.8211 (pm20) cc_final: 0.8004 (pm20) REVERT: C 889 MET cc_start: 0.8653 (mtp) cc_final: 0.8190 (mtt) outliers start: 33 outliers final: 22 residues processed: 182 average time/residue: 0.1410 time to fit residues: 38.0608 Evaluate side-chains 172 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 150 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 520 GLN Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain B residue 101 ASN Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 317 TRP Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 553 ILE Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 631 ILE Chi-restraints excluded: chain C residue 697 THR Chi-restraints excluded: chain C residue 733 THR Chi-restraints excluded: chain C residue 848 ARG Chi-restraints excluded: chain C residue 973 LYS Chi-restraints excluded: chain C residue 995 THR Chi-restraints excluded: chain D residue 65 ASP Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 298 GLU Chi-restraints excluded: chain D residue 326 THR Chi-restraints excluded: chain D residue 329 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 121 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 135 optimal weight: 0.1980 chunk 96 optimal weight: 3.9990 chunk 161 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 171 optimal weight: 6.9990 chunk 158 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 38 optimal weight: 0.3980 chunk 17 optimal weight: 5.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 961 ASN D 278 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.132525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.105633 restraints weight = 48396.530| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 2.33 r_work: 0.3065 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3068 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3068 r_free = 0.3068 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3068 r_free = 0.3068 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3068 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17482 Z= 0.143 Angle : 0.528 10.165 24182 Z= 0.289 Chirality : 0.041 0.167 2641 Planarity : 0.004 0.044 2672 Dihedral : 20.996 77.127 3316 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.50 % Favored : 96.44 % Rotamer: Outliers : 1.92 % Allowed : 12.45 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.20), residues: 1787 helix: 1.37 (0.22), residues: 568 sheet: 0.57 (0.30), residues: 311 loop : -1.19 (0.20), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 529 TYR 0.016 0.001 TYR A 757 PHE 0.029 0.001 PHE A 911 TRP 0.027 0.002 TRP B 317 HIS 0.004 0.001 HIS C 990 Details of bonding type rmsd covalent geometry : bond 0.00330 (17474) covalent geometry : angle 0.52494 (24178) hydrogen bonds : bond 0.03407 ( 768) hydrogen bonds : angle 4.13172 ( 2129) metal coordination : bond 0.00945 ( 8) metal coordination : angle 4.43485 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 165 time to evaluate : 0.571 Fit side-chains REVERT: A 602 MET cc_start: 0.8686 (mtp) cc_final: 0.8396 (mtp) REVERT: A 939 THR cc_start: 0.9106 (m) cc_final: 0.8825 (p) REVERT: B 55 LEU cc_start: 0.9130 (tp) cc_final: 0.8857 (tp) REVERT: C 649 GLU cc_start: 0.8137 (pm20) cc_final: 0.7913 (pm20) REVERT: C 889 MET cc_start: 0.8514 (mtp) cc_final: 0.8171 (mtt) outliers start: 27 outliers final: 24 residues processed: 187 average time/residue: 0.1386 time to fit residues: 38.8210 Evaluate side-chains 176 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 152 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 520 GLN Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain B residue 101 ASN Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain C residue 553 ILE Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 631 ILE Chi-restraints excluded: chain C residue 638 VAL Chi-restraints excluded: chain C residue 697 THR Chi-restraints excluded: chain C residue 733 THR Chi-restraints excluded: chain C residue 961 ASN Chi-restraints excluded: chain C residue 973 LYS Chi-restraints excluded: chain C residue 995 THR Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 65 ASP Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 298 GLU Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 326 THR Chi-restraints excluded: chain D residue 329 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 134 optimal weight: 0.9980 chunk 160 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 chunk 138 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 68 optimal weight: 6.9990 chunk 96 optimal weight: 0.0470 chunk 161 optimal weight: 0.0000 chunk 22 optimal weight: 0.8980 chunk 147 optimal weight: 6.9990 overall best weight: 0.5882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 961 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.133879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.107284 restraints weight = 55159.323| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 2.42 r_work: 0.3084 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3090 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3090 r_free = 0.3090 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3090 r_free = 0.3090 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3090 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17482 Z= 0.122 Angle : 0.511 10.658 24182 Z= 0.280 Chirality : 0.040 0.165 2641 Planarity : 0.004 0.043 2672 Dihedral : 20.893 78.448 3316 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.33 % Favored : 96.61 % Rotamer: Outliers : 1.66 % Allowed : 13.28 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.20), residues: 1787 helix: 1.53 (0.22), residues: 568 sheet: 0.74 (0.30), residues: 309 loop : -1.08 (0.20), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 148 TYR 0.017 0.001 TYR A 757 PHE 0.026 0.001 PHE A 911 TRP 0.022 0.001 TRP B 317 HIS 0.003 0.001 HIS C 990 Details of bonding type rmsd covalent geometry : bond 0.00275 (17474) covalent geometry : angle 0.50891 (24178) hydrogen bonds : bond 0.03167 ( 768) hydrogen bonds : angle 4.04683 ( 2129) metal coordination : bond 0.00772 ( 8) metal coordination : angle 3.95430 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 169 time to evaluate : 0.612 Fit side-chains REVERT: A 520 GLN cc_start: 0.8290 (OUTLIER) cc_final: 0.7809 (mt0) REVERT: A 602 MET cc_start: 0.8675 (mtp) cc_final: 0.8383 (mtp) REVERT: A 939 THR cc_start: 0.9059 (m) cc_final: 0.8826 (p) REVERT: B 51 LYS cc_start: 0.7712 (ptpp) cc_final: 0.7450 (mtpp) REVERT: B 55 LEU cc_start: 0.9123 (tp) cc_final: 0.8879 (tp) REVERT: C 649 GLU cc_start: 0.8044 (pm20) cc_final: 0.7795 (pm20) REVERT: C 889 MET cc_start: 0.8510 (mtp) cc_final: 0.8192 (mtt) REVERT: C 968 PHE cc_start: 0.8947 (t80) cc_final: 0.8610 (t80) outliers start: 23 outliers final: 20 residues processed: 188 average time/residue: 0.1347 time to fit residues: 38.1682 Evaluate side-chains 177 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 156 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 520 GLN Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain B residue 101 ASN Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain C residue 553 ILE Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 631 ILE Chi-restraints excluded: chain C residue 638 VAL Chi-restraints excluded: chain C residue 697 THR Chi-restraints excluded: chain C residue 733 THR Chi-restraints excluded: chain C residue 973 LYS Chi-restraints excluded: chain C residue 995 THR Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 65 ASP Chi-restraints excluded: chain D residue 298 GLU Chi-restraints excluded: chain D residue 326 THR Chi-restraints excluded: chain D residue 329 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 44 optimal weight: 0.9980 chunk 96 optimal weight: 0.0980 chunk 62 optimal weight: 5.9990 chunk 127 optimal weight: 0.9980 chunk 14 optimal weight: 4.9990 chunk 145 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 473 ASN ** C 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 961 ASN D 101 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.132794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.105578 restraints weight = 56627.547| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 2.44 r_work: 0.3075 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3076 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3076 r_free = 0.3076 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3076 r_free = 0.3076 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3076 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17482 Z= 0.136 Angle : 0.519 10.568 24182 Z= 0.283 Chirality : 0.040 0.165 2641 Planarity : 0.004 0.042 2672 Dihedral : 20.900 79.546 3316 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.72 % Favored : 96.22 % Rotamer: Outliers : 2.04 % Allowed : 12.84 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.20), residues: 1787 helix: 1.59 (0.22), residues: 568 sheet: 0.76 (0.29), residues: 317 loop : -0.98 (0.20), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 529 TYR 0.015 0.001 TYR A 757 PHE 0.029 0.001 PHE A 911 TRP 0.024 0.002 TRP B 317 HIS 0.004 0.001 HIS C 990 Details of bonding type rmsd covalent geometry : bond 0.00311 (17474) covalent geometry : angle 0.51602 (24178) hydrogen bonds : bond 0.03285 ( 768) hydrogen bonds : angle 4.03471 ( 2129) metal coordination : bond 0.00832 ( 8) metal coordination : angle 4.27724 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 158 time to evaluate : 0.424 Fit side-chains REVERT: A 520 GLN cc_start: 0.8241 (OUTLIER) cc_final: 0.7772 (mt0) REVERT: A 602 MET cc_start: 0.8676 (mtp) cc_final: 0.8402 (mtp) REVERT: A 939 THR cc_start: 0.9085 (m) cc_final: 0.8834 (p) REVERT: B 51 LYS cc_start: 0.7781 (ptpp) cc_final: 0.7535 (mtpp) REVERT: C 649 GLU cc_start: 0.8027 (pm20) cc_final: 0.7793 (pm20) REVERT: C 849 MET cc_start: 0.8621 (ttm) cc_final: 0.8348 (tpp) REVERT: C 889 MET cc_start: 0.8511 (mtp) cc_final: 0.8211 (mtt) REVERT: C 968 PHE cc_start: 0.8869 (t80) cc_final: 0.8532 (t80) outliers start: 29 outliers final: 26 residues processed: 180 average time/residue: 0.1329 time to fit residues: 36.0504 Evaluate side-chains 181 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 154 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 473 ASN Chi-restraints excluded: chain A residue 520 GLN Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain B residue 101 ASN Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain C residue 553 ILE Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 602 MET Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 631 ILE Chi-restraints excluded: chain C residue 638 VAL Chi-restraints excluded: chain C residue 697 THR Chi-restraints excluded: chain C residue 715 VAL Chi-restraints excluded: chain C residue 733 THR Chi-restraints excluded: chain C residue 961 ASN Chi-restraints excluded: chain C residue 973 LYS Chi-restraints excluded: chain C residue 995 THR Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 65 ASP Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 298 GLU Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 326 THR Chi-restraints excluded: chain D residue 329 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 100 optimal weight: 4.9990 chunk 3 optimal weight: 0.0030 chunk 127 optimal weight: 2.9990 chunk 49 optimal weight: 0.2980 chunk 0 optimal weight: 3.9990 chunk 183 optimal weight: 3.9990 chunk 128 optimal weight: 0.8980 chunk 2 optimal weight: 0.7980 chunk 146 optimal weight: 3.9990 chunk 70 optimal weight: 0.9980 chunk 32 optimal weight: 0.0030 overall best weight: 0.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 473 ASN ** C 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 961 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.134671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.108123 restraints weight = 59778.798| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 2.50 r_work: 0.3090 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3090 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3090 r_free = 0.3090 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3090 r_free = 0.3090 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3090 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 17482 Z= 0.111 Angle : 0.500 11.014 24182 Z= 0.273 Chirality : 0.039 0.163 2641 Planarity : 0.004 0.042 2672 Dihedral : 20.836 80.005 3316 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.16 % Favored : 96.78 % Rotamer: Outliers : 1.92 % Allowed : 13.41 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.20), residues: 1787 helix: 1.69 (0.23), residues: 567 sheet: 0.83 (0.29), residues: 318 loop : -0.87 (0.20), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 529 TYR 0.016 0.001 TYR A 757 PHE 0.028 0.001 PHE A 911 TRP 0.019 0.001 TRP B 317 HIS 0.002 0.001 HIS C 990 Details of bonding type rmsd covalent geometry : bond 0.00246 (17474) covalent geometry : angle 0.49799 (24178) hydrogen bonds : bond 0.03023 ( 768) hydrogen bonds : angle 3.96756 ( 2129) metal coordination : bond 0.00689 ( 8) metal coordination : angle 3.55336 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 166 time to evaluate : 0.577 Fit side-chains REVERT: A 520 GLN cc_start: 0.8239 (OUTLIER) cc_final: 0.7797 (mt0) REVERT: A 602 MET cc_start: 0.8684 (mtp) cc_final: 0.8438 (mtp) REVERT: A 939 THR cc_start: 0.9040 (m) cc_final: 0.8828 (p) REVERT: C 649 GLU cc_start: 0.7986 (pm20) cc_final: 0.7750 (pm20) REVERT: C 889 MET cc_start: 0.8486 (mtp) cc_final: 0.8218 (mtt) REVERT: C 968 PHE cc_start: 0.8864 (t80) cc_final: 0.8541 (t80) outliers start: 27 outliers final: 20 residues processed: 184 average time/residue: 0.1456 time to fit residues: 40.2204 Evaluate side-chains 180 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 159 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 520 GLN Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain B residue 101 ASN Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain C residue 553 ILE Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 631 ILE Chi-restraints excluded: chain C residue 638 VAL Chi-restraints excluded: chain C residue 697 THR Chi-restraints excluded: chain C residue 715 VAL Chi-restraints excluded: chain C residue 733 THR Chi-restraints excluded: chain C residue 973 LYS Chi-restraints excluded: chain C residue 995 THR Chi-restraints excluded: chain D residue 65 ASP Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 298 GLU Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 326 THR Chi-restraints excluded: chain D residue 329 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 107 optimal weight: 0.5980 chunk 149 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 10 optimal weight: 0.3980 chunk 12 optimal weight: 0.6980 chunk 150 optimal weight: 5.9990 chunk 134 optimal weight: 0.9980 chunk 74 optimal weight: 6.9990 chunk 9 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 961 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.134047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.106804 restraints weight = 65892.156| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.66 r_work: 0.3078 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3081 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3081 r_free = 0.3081 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3081 r_free = 0.3081 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3081 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17482 Z= 0.123 Angle : 0.507 10.785 24182 Z= 0.276 Chirality : 0.040 0.166 2641 Planarity : 0.004 0.042 2672 Dihedral : 20.831 80.602 3316 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.78 % Favored : 96.16 % Rotamer: Outliers : 1.98 % Allowed : 13.41 % Favored : 84.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.20), residues: 1787 helix: 1.67 (0.23), residues: 574 sheet: 0.93 (0.29), residues: 318 loop : -0.82 (0.21), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 529 TYR 0.015 0.001 TYR A 757 PHE 0.028 0.001 PHE A 911 TRP 0.021 0.001 TRP B 317 HIS 0.003 0.001 HIS C 990 Details of bonding type rmsd covalent geometry : bond 0.00281 (17474) covalent geometry : angle 0.50469 (24178) hydrogen bonds : bond 0.03139 ( 768) hydrogen bonds : angle 3.94940 ( 2129) metal coordination : bond 0.00753 ( 8) metal coordination : angle 4.05855 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 161 time to evaluate : 0.561 Fit side-chains REVERT: A 520 GLN cc_start: 0.8233 (OUTLIER) cc_final: 0.7789 (mt0) REVERT: A 602 MET cc_start: 0.8669 (mtp) cc_final: 0.8411 (mtp) REVERT: A 939 THR cc_start: 0.9077 (m) cc_final: 0.8837 (p) REVERT: B 152 MET cc_start: 0.8830 (tpt) cc_final: 0.8588 (tpt) REVERT: C 649 GLU cc_start: 0.7989 (pm20) cc_final: 0.7719 (pm20) REVERT: C 858 MET cc_start: 0.8607 (mmt) cc_final: 0.8401 (mmt) REVERT: C 889 MET cc_start: 0.8496 (mtp) cc_final: 0.8233 (mtt) outliers start: 28 outliers final: 22 residues processed: 181 average time/residue: 0.1352 time to fit residues: 36.3127 Evaluate side-chains 181 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 158 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 520 GLN Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain B residue 101 ASN Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain C residue 553 ILE Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 631 ILE Chi-restraints excluded: chain C residue 638 VAL Chi-restraints excluded: chain C residue 715 VAL Chi-restraints excluded: chain C residue 733 THR Chi-restraints excluded: chain C residue 973 LYS Chi-restraints excluded: chain C residue 995 THR Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 65 ASP Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 298 GLU Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 326 THR Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 335 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 24 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 114 optimal weight: 3.9990 chunk 168 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 chunk 125 optimal weight: 0.0470 chunk 146 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 71 optimal weight: 0.4980 overall best weight: 1.0282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 961 ASN D 54 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.132170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.104875 restraints weight = 56654.427| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 2.55 r_work: 0.3054 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3056 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3056 r_free = 0.3056 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3056 r_free = 0.3056 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3056 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17482 Z= 0.154 Angle : 0.540 10.795 24182 Z= 0.292 Chirality : 0.041 0.183 2641 Planarity : 0.004 0.046 2672 Dihedral : 20.943 81.204 3316 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.01 % Favored : 95.94 % Rotamer: Outliers : 1.85 % Allowed : 13.67 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.20), residues: 1787 helix: 1.64 (0.22), residues: 568 sheet: 0.93 (0.29), residues: 318 loop : -0.83 (0.20), residues: 901 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 529 TYR 0.015 0.001 TYR A 805 PHE 0.027 0.001 PHE A 911 TRP 0.025 0.002 TRP B 317 HIS 0.004 0.001 HIS C 990 Details of bonding type rmsd covalent geometry : bond 0.00359 (17474) covalent geometry : angle 0.53649 (24178) hydrogen bonds : bond 0.03446 ( 768) hydrogen bonds : angle 4.03259 ( 2129) metal coordination : bond 0.00848 ( 8) metal coordination : angle 4.50177 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 161 time to evaluate : 0.562 Fit side-chains REVERT: A 520 GLN cc_start: 0.8228 (OUTLIER) cc_final: 0.7769 (mt0) REVERT: A 602 MET cc_start: 0.8678 (mtp) cc_final: 0.8448 (mtp) REVERT: A 636 GLN cc_start: 0.8112 (mp10) cc_final: 0.7771 (mp10) REVERT: A 939 THR cc_start: 0.9095 (m) cc_final: 0.8829 (p) REVERT: B 152 MET cc_start: 0.8847 (tpt) cc_final: 0.8629 (tpt) REVERT: C 649 GLU cc_start: 0.8095 (pm20) cc_final: 0.7838 (pm20) REVERT: C 858 MET cc_start: 0.8649 (mmt) cc_final: 0.8441 (mmp) REVERT: C 889 MET cc_start: 0.8530 (mtp) cc_final: 0.8259 (mtt) outliers start: 26 outliers final: 25 residues processed: 181 average time/residue: 0.1393 time to fit residues: 37.9327 Evaluate side-chains 180 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 154 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 520 GLN Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain B residue 101 ASN Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 301 GLU Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain C residue 553 ILE Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 631 ILE Chi-restraints excluded: chain C residue 638 VAL Chi-restraints excluded: chain C residue 697 THR Chi-restraints excluded: chain C residue 715 VAL Chi-restraints excluded: chain C residue 733 THR Chi-restraints excluded: chain C residue 961 ASN Chi-restraints excluded: chain C residue 973 LYS Chi-restraints excluded: chain C residue 995 THR Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 65 ASP Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 298 GLU Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 326 THR Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 335 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 6 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 60 optimal weight: 20.0000 chunk 112 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 124 optimal weight: 0.5980 chunk 162 optimal weight: 6.9990 chunk 101 optimal weight: 4.9990 chunk 138 optimal weight: 0.6980 chunk 81 optimal weight: 0.5980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 961 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.130330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.102782 restraints weight = 50953.990| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 2.65 r_work: 0.3042 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3042 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3042 r_free = 0.3042 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3042 r_free = 0.3042 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3042 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 17482 Z= 0.204 Angle : 0.575 10.573 24182 Z= 0.309 Chirality : 0.043 0.173 2641 Planarity : 0.005 0.053 2672 Dihedral : 21.055 81.485 3315 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.12 % Favored : 95.82 % Rotamer: Outliers : 1.85 % Allowed : 13.60 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.20), residues: 1787 helix: 1.49 (0.22), residues: 569 sheet: 0.86 (0.29), residues: 318 loop : -0.91 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 529 TYR 0.017 0.002 TYR A 805 PHE 0.027 0.002 PHE A 911 TRP 0.025 0.002 TRP B 317 HIS 0.005 0.001 HIS C 990 Details of bonding type rmsd covalent geometry : bond 0.00483 (17474) covalent geometry : angle 0.57115 (24178) hydrogen bonds : bond 0.03847 ( 768) hydrogen bonds : angle 4.13894 ( 2129) metal coordination : bond 0.00972 ( 8) metal coordination : angle 5.02856 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3845.92 seconds wall clock time: 66 minutes 35.01 seconds (3995.01 seconds total)